|
| Status |
Public on Mar 11, 2014 |
| Title |
5C0077T |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
tumor DNA from esophageal
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age: 68
survival (days): 143
tnm: T3N1M0
tissue type: esophageal tumor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA samples were isolated using a QIAamp DNA Mini Kit according to the manufacturer’s instructions (Qiagen, Germantown, MD).
|
| Label |
Cy3
|
| Label protocol |
Equal amounts of the test DNA (1 μg or 0.5 μg) and reference DNA (1 μg or 0.5 μg), were digested with AluI and RsaI. The digested test DNA and reference DNA were labeled with cyanine (Cy)5-deoxyuridine triphosphate (dUTP) or Cy3-dUTP, respectively, using the SureTag Complete DNA Labeling Kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
normal DNA from blood
|
| Organism |
Homo sapiens |
| Characteristics |
gender: F
age: 68
survival (days): 143
tnm: T3N1M0
tissue type: normal blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA samples were isolated using a QIAamp DNA Mini Kit according to the manufacturer’s instructions (Qiagen, Germantown, MD).
|
| Label |
Cy5
|
| Label protocol |
Equal amounts of the test DNA (1 μg or 0.5 μg) and reference DNA (1 μg or 0.5 μg), were digested with AluI and RsaI. The digested test DNA and reference DNA were labeled with cyanine (Cy)5-deoxyuridine triphosphate (dUTP) or Cy3-dUTP, respectively, using the SureTag Complete DNA Labeling Kit (Agilent).
|
| |
|
| |
| Hybridization protocol |
The Cy3-labeled test DNA and Cy5-labeled reference DNA were mixed and combined with 2× Hybridization buffer, 10× blocking agent (Agilent), and Human Cot-1 DNA. The hybridization mixture was dispensed to a microarray chip and assembled with an Agilent SureHyb chamber. The assembled slide chamber was placed in the rotator rack in a hybridization oven set to 65°C for 40 hours with suitable rotation.
|
| Scan protocol |
Arrays were scanned on a were scanned on an Agilent Microarray Scanner G2565C with 2-μm resolution.
|
| Description |
Esophageal Cancer Project
|
| Data processing |
Data were extracted from scanned images using the Feature Extraction software, version 11 (Agilent). The text files were then imported for analysis into Genomic Workbench, lite edition 6.5 (Agilent).
Final vaues are reported as 'log2 (EXP_NORM/REF_NORM)' in linked supplementary files.
|
| |
|
| Submission date |
Feb 13, 2014 |
| Last update date |
Mar 12, 2014 |
| Contact name |
Lin Li |
| E-mail(s) |
[email protected]
|
| Organization name |
BGI
|
| Street address |
Beishan Industrial Zone
|
| City |
shenzhen |
| ZIP/Postal code |
518083 |
| Country |
China |
| |
|
| Platform ID |
GPL8736 |
| Series (2) |
| GSE54993 |
a-CGH of Esophageal Cancer (70 cases) |
| GSE54995 |
Esophageal Cancer Project |
|
